as_pfs_os function

Convert multi-state data to PFS and OS data

Convert a multi-state dataset with irreversible transitions containing 3 health states to a dataset with one row per patient and progression-free survival (PFS) and overall survival (OS) time-to-event outcomes.

as_pfs_os(
  data,
  patient_vars,
  status = "status",
  time_stop = "time_stop",
  transition = "transition_id"
)

Arguments

• data: A multi-state dataset.
• patient_vars: Character vector of the names of patient specific variables.
• status: Character string with the name of the status variable (1 = event, 0 = censored).
• time_stop: Character string with the name of the stopping time variable (i.e., time patient transitions from state $r$ to state $s$).
• transition: Character string with the name of the variable identifying a transition. The transition variable should be integer valued with values 1, 2, and 3 for the Stable -> Progression, Stable -> Death, and Progression -> Death transitions, respectively.

Returns

A data.table with one row per patient containing each variable in patient_vars as well as a time variable and status indicator for both PFS (pfs_status, pfs_time) and OS (os_time, os_status).

Examples

as_pfs_os(onc3, patient_vars = c("patient_id", "strategy_name", "female", "age"))